Just to confirm - within [Game Folder]\www\save\ you have config.rpgsave (if you've modified the settings), save1.rpgsave, and global.rpgsave, right?
I'd recommend creating a "backup" folder. Put all the files from [Game Folder]\www\save\ into that, then start a new game and save into whatever slot the save you're trying to recover is in (so slot 1 in your case). Copy your save1.rpgsave from the backup folder and overwrite the one in the save folder. Unless that save file is broken/corrupted, it should work (I tested with my save files). If the save file is broken/corrupted, you've probably lost all your progress - but on the bright side, it's fairly easy to get back where you were, now that you know what to do. Oh, and your computer may be having issues, such as a virus, a too-full harddrive, a harddrive that's on its last legs, etc.